Ruby's Secret
by Aubrie1234
Summary: During their adventures, Ruby and Sapphire meet up again, but get captured by the new teamed-up Team Magma and Aqua. Ruby helps Sapphire escape, but reveals a secret he would have loved to leave behind in his past. The story also has a different past for Ruby. IS BEING REWRITTEN.
1. Chapter 1

Ruby's Secret

By:Aubrie1234

**Dear Readers, I've had this idea on my mind for a while, so I decided to finally post it. Franticshipping fanfic. And the story shall start now!**

Ruby and Sapphire had stopped their rivalry for a while, to just travel together, but then came across Team Magma and Team Aqua. They had teamed up to steal something, but weren't revealing what they were stealing. As soon as she saw them, Sapphire wanted to fight them and make them stop. Ruby, on the other hand, suggested that they spy on them and find out what they were up to. Sapphire reluctantly agreed, knowing that it would be best to find out what was happening. That then led up to where they were now, in the trees spying on them. Sapphire was used to being in the trees, but Ruby wasn't. She managed to keep both of them balanced while they spied, which wasn't easy. Every so often, she might lose her balance, but Ruby would help her. It was amazing to Sapphire at how Ruby could keep his balance. It was also a bit of a miracle that they hadn't gotten caught yet, since they had already stayed up there for twenty minutes already. A few members of Team Aqua were right underneath them, while Team Magma was nowhere in sight.

"Who are we going after again, sir?" one of the grunts asked the Team Aqua Admin that was with them right then, which was Shelly.

"Archie said that we're going after those two kids that keep ruining our plans. Either he wants them out of our way, or something else. He really didn't say what he and Team Magma's boss are going to do to them once they're caught, but I'm only guessing." she answered, then told them to spread out and find them. Sapphire and Ruby then exchanged worried glances, knowing that they were going to be in big trouble if they were caught. After Team Aqua left, they decided to get out of there. Soon, they were nearly out of range from the two team's search area. But, unfortunately, someone attacked them from behind and knocked Sapphire out. Ruby had dodged the attack, but couldn't see the attacker because of the darkness.

_Whoever attacked us chose the right place to do so, since the nearest lights are the streetlamps, which are still too far away. _Ruby thought as he glanced around, looking for their attacker. He was angry a little bit since he couldn't see who was attacking them, and that Sapphire was knocked out. He needed to protect her and himself from whoever knocked her out and was still attacking them. Whoever was attacking them was also using a very fast pokemon as well. If it was fast that he hadn't noticed until it knocked out Sapphire then it had to be extremely fast. Suddenly, he saw a flash of green and white with a tint of red off to his right, then close to his left. He knew he didn't have time to bring out his pokedex or pokemon before it attacked, so he braced himself. Then, Ruby felt a sharp stab in his left shoulder, making his grab it and shout in pain. He looked at the wound and recognized it as a Drain Punch. Only a fighting-type pokemon with lots of speed or a pokemon that could learn Drain Punch also with lots of speed could have made that wound.

_But, _he thought, covering the wound back up with his hand, gritting his teeth in pain, and looking around sharply, _both Team Magma and Team Aqua usually don't have a fighting-type pokemon or a pokemon that could learn fighting-type moves. Who could be attacking me, then? _Just as he thought that, he felt a sharp pain right behind him, beneath his neck, before blacking out.

* * *

Soon, Ruby felt himself come to. He felt a dull throb coming from the injury on his shoulder and right below his neck, where, he thought, another Drain Punch had hit him. As he slowly opened his eyes, he saw soft moonlight came through a blind-covered window to his right, the moonlight landing right in front of him. He slowly looked around, making sure to not hurt his injuries more than they were already. The room he was in was small, only big enough to house five or six people at most. It had metal walls that looked brand new, along with a thick-looking metal door. The door looked like it was strong and thick enough to keep in anything, even an angry Slaking. As he looked around, he saw Sapphire (who was still knocked out) beside him, lying on her right side. She looked like she hadn't gotten hurt since last time, and that was a great relief to Ruby. But, as he looked her over (checking for any scratches he might have missed), he saw that she had her arms tied behind her back, along with her feet being tied together as well. Now that he thought about it, he was probably tied up the same way as well. He tried to move, but, just as he thought, he couldn't move.

"Just great." he sighed, starting to talk to himself, "First, we run into the teamed-up Team Aqua and Magma, get attack by a mysterious person or pokemon, and now we're locked up, probably by the same person, pokemon, or by Team Aqua and Magma. How do I get dragged into all of these things, anyway?" Ruby then looked up at the door and saw that it had a small window on it, located about four-fifths of the way up. He tried to look through it the best he could (since he was still tied up and couldn't move), but couldn't see anything. He then looked towards the unconscious form of his friend and rival. He got a sad expression on his face, tears welling up in his eyes as he quickly turned away.

"I know you aren't awake, Saph, but I wanted to tell you that I never wanted you to get caught in the first place. You mean the world to me, even though I would never openly admit it. I'll get you out, I promise. And when I make a promise in a situation like this one, I mean it. I _will_ get you out, no matter what." Ruby confessed, tears trailing down his cheeks. Besides what he confessed, he was also pained to see her tied up and unconscious. She never deserved to be put in a situation like this. She was meant to be out, fighting battles and Gym Leaders with her pokemon while he made cute accessories and participated in pokemon contests.

_I need to get her out, but how? _he thought, looking up. As he looked up, he caught sight of the blind-covered window and the moonlight shining through.

_I know I'm taking a big risk if I do it, but I don't have any other choice. _he then thought, getting a determined look on his face.

* * *

Meanwhile, with Team Magma and Aqua's bosses:

"Maxie, I know those kids are very annoying by disrupting our plans, but give the explanation of _why_ it was so important we captured them, will you?" Archie, Team Aqua's boss, asked the man sitting opposite of him, across the table.

"The reason why is because one of those kids looks very familiar, don't you think, Archie? Remember back when we were young and were still scientists apart of Team Steam?" Maxie, the head of Team Magma, asked him.

"Of course I do! How could I ever forget those days? And are you saying that one of those kids-" he said, but was interrupted by Maxie.

"-was the one who had escaped and cost Team Steam everything it had? Yes. I think that the kid with the white hat is the one, Archie. Even if he or the girl aren't the one, we can still have our revenge on them after what they have done to our plans." he continued.

"I plan on getting revenge on them either way. They nearly blew our cover as the supposed 'good guys,' trying to give _good_ changes to the region. They both need to be taught a lesson in trying to stop us."

"Agreed. And, if either of them is the one, we can also teach him/her to not run away from us again. This time, he/she _isn't_ going to escape." Maxie explained.

* * *

_**Uh oh. That doesn't sound good. And what is Ruby going to do? Find out in the next chapter, guys!**_


	2. Chapter 2

Ruby's Secret

By:Aubrie1234

Suddenly, a blood-curdling roar sounded throughout the whole ship, scaring everyone. But the bosses knew who it was.

"Looks like you were right, Maxie. Our little friend really is here." Archie said, getting out of his seat and heading to the door.

"Yes, and this time, we're going to make sure he/she doesn't get away again." Maxie answered him, following him out.

* * *

Elsewhere on the ship:

A giant Mightyena-like pokemon stood in the broken doorway of a holding cell, its eyes glinting in the moonlight. Like a regular Mightyena, it had black hair flowing down its back in two identical stripes. It also had a Mightyena-like body. But that's where the similarities ended. It had white fur instead of gray, its eyes were ruby-red in color, stood on two legs, managed to talk, and it had gray, bat-like wings. It let out a tremendous roar once again, then looked back to the girl that was also in the cell. She was staring to wake up, but was still tied.

"Ngh... W-where am I?" she said groggily. Her head hurt and she wasn't fully awake yet. She then heard a soft growl come from in front of her. Her eyes shot open as she saw the strange creature in front of her, staring at her and holding five pokeballs in its clawed hands. She cringed a little in fright. Unlike most pokemon, this one scared her for real. It tilted its head in confusion at her actions.

"What are ya going to do?" she asked, trying to hide the fear in her voice. It slowly put the pokeballs on the ground and reached over her. She heard cutting noises and felt her hands get loose. After that, it reached down to her feet and cut off the ropes there. Afterwords, Sapphire sat up, rubbing her wrists and ankles because of the rope marks on them, trying to soften the soreness.

"Thank you." she told the creature. It then picked up the pokeballs and held them out to her expectantly.

"Why are ya-?" she wasn't able to finish because it then dropped the pokeballs in her lap and stood protectively in front of her.

"What is that thing?" she heard someone say.

"I don't know, but it's trying to free one of the kids! Crawdaunt, Hydro Pump!" Suddenly, the creature crossed its arms as a giant and hard-hitting stream of water hit it. It was pushed back a bit, but broke the attack. Then, it jumped at the Rogue Pokemon and punched it, sending it into the wall. Even though the wall was thick and made of steel, the attack left a very noticeable dent in it. Crawdaunt's trainer then returned it as the other trainer brought out her pokemon: a Slugma.

"Slugma, Eruption!" Then, the pokemon let out a giant stream of fire at the creature. It blocked the attack, then broke through and did the same to it as it did to the Crawdaunt. The pokemon was returned, and the two members ran away, probably to get reinforcements. The pokemon then looked tiredly at Sapphire, a tinge of sadness shining in its eyes.

"Thank you, again. But, why are ya sad?" she asked the creature. It just looked back at the door and started towards it, making motions to her so that she followed. She did as she was told and they went down the long halls, trying to find a way out. Soon, they found themselves at a fork.

"Which way do we go now?" she sighed, mostly to no-one. The creature walked in front of each doorway, and went to the right one. It looked back at her, then looked back down the hallway as it walked.

"Hey! Wait for me!" Sapphire yelled as she caught up.

_The creature sure is quiet. I wonder why. Whoever it is acts a lot like Ruby. And I wonder where Prissy Boy is. For once I miss him. _she thought.

"Hey." she asked. The creature looked at her without turning its head as she continued. "Do ya know where a boy named Ruby is? He has red eyes like you and wears a long hat. He also loves contests and fashion." It closed its eyes and continued walking, not answering her.

_Some help that was._ she then thought. Suddenly, she then heard the creature speak.

"No. I don't know where he is. But outside is this way." it said. It was easily recognizable as a boy's voice, similar to Ruby's.

"How did ya know I was here, anyway?" He smirked.

"Call me a stalker if you want, but I like to think of it as a Guardian Angel for you."

"Well, thanks again for saving me from those teamed-up freaks. But I don't remember how I was knocked out."

"Breloom."

"What did ya say?"

"Breloom. It's a fighting and grass-type pokemon. It attacked you and your friend with Drain Punch while you were spying on the 'teamed-up freaks.' Then you were both captured and brought here."

"How did ya know that?" He then smirked again.

"I have my ways."

"And why did ya give me these pokeballs? They're not even mine!"

"They're Ruby's. He wanted them to be safe, but couldn't get away. He gave them to me for safekeeping, but I think you would be better for it."

"Why me?"

"Because, I have something to settle with Team Aqua's and Magma's bosses but I can't keep his pokeballs. You were his second suggestion if I couldn't do it."

"Again, why me?" He sighed.

"Because, I think he holds a special place in his heart for you. He loves you, Sapphire."

"Me?!"

"Yes, you. He wanted me to get you out first, even if it meant that he wouldn't escape. He never wanted you to get captured in the first place. He even thinks it's his fault for not saving you."

"It isn't his fault. We didn't know it was there. He shouldn't blame himself for my capture." It was quiet between those two for another few minutes until the creature said: "Anyway, we're almost there." Once they reached the outside, they could see that it was clearly nighttime and had a full moon out. They rushed to the side of the ship and Sapphire brought out her Wailord, Lorry.

"Don't you dare leave, kids." someone said from behind them. The creature whipped around and put up a protective stance in front of Sapphire, growling angrily and loudly. When Sapphire turned, she saw the bosses of Team Magma and Aqua behind them, their pokemon already out.

"You aren't going to get away with ruining our plans this time. Camerupt, Overheat!" Maxie said, ordering his Camerupt. It powered up its move while Archie told his Crawdaunt to use Hydro Pump. The creature braced itself for the attacks as he told Sapphire: "Get on Lorry, now!" She obeyed and jumped, landing on its back safely. She looked up to the edge of the ship, seeing the attacks flying over the railing.

_He must have dodged it. Good. I hope he gets on Lorry before he's hurt too much. _Sapphire thought. But, the attacks were fired again and an explosion happened. The whole place was covered in smoke except her and Lorry. Then, she saw something fall from the cloud and land with a hard 'thump' on Lorry. It was the creature, and he seemed to be in pain, holding his right shoulder. Sapphire told Lorry to head to Littleroot Town as she ran to help him.

"Hey! Are ya alright?" she asked. He slowly took its hand of the injury and showed her. There was a patch of charred fur, black as charcoal and with a small stream of smoke coming off it. Sapphire winced.

"I-I'll be fine. Where are we going, anyway?" he asked, wincing as he covered the injury again.

"Littleroot Town. By the way, how did you know Lorry's name? I never told ya."

"Like I told you before, I'm your Guardian Angel. I should know the name of you and your pokemon at least, shouldn't I?" he grinned as he said that.

"Yeah, well, my name's Sapphire. What's your's?" she asked him. He hesitated for a moment before saying: "Silver."

"Great. Dad will want ta see ya on that injury, too. Don't worry, he's nice. But ya probably already know that, don't ya?" Sapphire told him, smiling. He smiled back, saying: "I do. And thank you for taking to him."

"You're welcome." she told him as they started the long journey from there to Littleroot.

* * *

_**Second chapter, I know. Well, what do you think? Tell me in a review, please!**_


	3. Chapter 3

Ruby's Secret

By: Aubrie1234

They rode Lorry all the way to Littleroot Town, nonstop. As they did, Silver's injury seemed to get worse. It hurt him badly whenever he tried to move it, which was a big mistake on his part.

"Ngh." Silver said as he moved a little, wincing at the pain.

"Stop moving already! If ya keep moving whenever ya don't need to, you're gonna hurt something much more than your shoulder!" Sapphire scolded him. He just looked her in the eyes for a minute, then turned away. Sapphire sighed.

"Your not gonna listen to me, are ya?" she said. Silver just closed his eyes and said: "When are we going to get there?"

"I don't know, but ya shouldn't have changed the subject!" Sapphire told him.

"Hmph. I have a right to change it if I want." Silver retorted.

"Never mind." Sapphire sighed, going back to the front of Lorry.

_I wish I could tell you the truth, Sapphire. I wish I could. _Silver thought, looking at her retreating form. Soon, they reached Littleroot Town. Sapphire helped Silver get off Lorry before returning her pokemon. They walked slowly the rest of the way. A few times Silver might slow down a little, trudging behind Sapphire. He had a painful expression on when that happened. Sapphire would wait for him to catch up before walking again.

"Ya know," Sapphire started as they walked, "Ya don't have ta walk the whole way. I could bring out one of my pokemon ta carry ya the rest of the way."

"No. I told you before that I'm fine." Silver told her as he walked ahead.

_Why doesn't he open up ta me? I've helped him ever since he saved me, but he's just been trying ta get farther away. _Sapphire thought.

"Hey. Don't daydream and get over here. We've still got a ways to go." Silver interrupted, looking back at her. She shook her head then ran up to him. The rest of the walk was spent in silence.

* * *

Soon, they reached Prof. Birch's lab. As Prof. Birch and his assistant bandaged Silver, Sapphire told them what had happened.

"...and that's what happened, Papa. Is Silver gonna be alright?" Sapphire ended, then asked.

"I don't know, but he should be well enough to leave in a few days. And I hope that Ruby is okay." Birch told her.

"Me too. Even Prissy Boy might not be able to figure a way out." Sapphire said.

_If she only knew. _Silver thought. He grimaced as they tightened the bandage.

"There. Until you heal enough to defend yourself, you need to stay here. Alright, Silver?" Birch's assistant asked.

"Yes sir." he said. The next few days were spent trying to help Silver adjust to his injury. Right now he was practicing to walk on all fours without putting too much pressure on the injured shoulder.

"Ngh. It still hurts." he growled out as he moved his arm.

"Well, don't whine about it and try again!" Sapphire growled back.

"Prissy Wolf." she muttered under her breath. Silver heard that and perked up slightly. If she had looked closer, she would've seen a small smile form on his muzzle.

_If she only knew how close she was with that statement. _Silver thought, walking again. He didn't whine as much after that, but still teased Sapphire into saying 'Prissy Wolf'.

* * *

_**Yes! Third chapter finished! Give me a review and I'll see you next chapter!**_


	4. Chapter 4

Ruby's Secret

By: Aubrie1234

"Ugh! Why don't ya leave me alone! Yer done healin' and can go, but ya don't stop followin' me!" Sapphire snapped at Silver. They were both on the outskirts of Littleroot and she had been trying to train when she had found out he had followed her, again.

"Like I said, I'm here as your Guardian Angel. I can't let you get hurt." he told her, shaking his head. Even after he had healed from his injury a few days ago, like Sapphire said, he wouldn't leave Littleroot for some reason (or, as he claimed, to protect her).

"I don't need protectin'! Chic and my other pokemon can do that! Ya need ta hide away from those teamed-up freaks, not stay here with me!" Silver flapped his wings in irritation.

"Saph, look-"

"Don't start, Prissy Wolf! You're nearly as bad as Ruby! Now, go hide and-"

"Sapphire..."

"-after they get defeated I can help ya-"

"_Sapphire_..."

"-and after that I can go and-"

"SAPPHIRE! STOP. TALKING!" Silver roared, his red eyes burning in anger. If she had only listened to him then they wouldn't be arguing right now! Sapphire flinched and hung her head. Silver, unlike most pokemon, scared her. Kind of like Salamences, but not as bad.

"Listen, alright?! I am only here to protect you and Ruby from danger and I failed my job with him! I have to protect you with my life to make up for my mistake, so I can't leave! Do you understand now?! I can't go because of what I have to! No-one else can do it, NO-ONE!" he roared again. Sapphire shrunk back in fear. Silver noticed this and he softened a little.

"I'm sorry I scared you, Saph. Just please, let me stay. I-" he started, but stopped and his ears perked up. He moved his head side-to-side, swiveling his ears, and strained to listen for something.

"What are ya-"

"Quiet!" Silver hissed at her before trying to listen again. Suddenly, a net came out of the bushes and landed on Silver, trapping him. He roared and struggled, trying to get out and yelling: "Sapphire! Run!" But, being stubborn, she wasn't going to let her friend get caught. She pulled out a pokeball and yelled: "Chic, use Sky Uppercut to free Silver!" The Blaziken came out and was about to punch the net with her attack when a Hydro Pump came out of the same bushes and struck her. She cried out in surprise and pain and skidded back, her claws digging into the ground to stop her from going farther.

_So stubborn! I told her to run! _Silver thought, still trying to get out. Then, the net suddenly was shocked with electricity and him in it.

"RRRAAAAAAHHHHH!" he shouted in pain. It stopped, but he hurt badly. He was panting, slightly heavy.

"Silver! Chic, use-" Sapphire started before they were both covered in another net.

"Not so fast, girly." someone spoke. Then, a Swellow flew up and showed Team Magma Admin Courtney in its claws. A Manectric, who was holding both nets in its teeth, walked out of the bushes and growled, soon followed by Team Aqua Admin Shelly and her Ludicolo.

"This time we've got both of you and you aren't going to escape." Shelly told her. Sapphire growled. They had just been sitting Psyducks in a waiting trap!

"If you do try to escape while these nets have you, Manectric will easily shock both of you relentlessly. I suggest you don't do that." Courtney said to them, blowing her bubblegum.

"Why...why do you want us?" Silver panted. The electric attack was taking more of a toll on him than he expected. His arms were shaking slightly in fatigue, but no-one noticed.

"_We_ don't, but our bosses do. Especially after you both escaped last time." Shelly explained.

"Yeah. You both made them _super _mad and they almost took it out on us!" Courtney added.

"Then why didn't ya leave?! Ya could have easily avoided that if ya had quit!" Sapphire told them in anger.

"We don't have anywhere else to go if we did. This is our only choice right now." Shelly told her harshly while Courtney glared.

"Yes...you do. You...just can't see it." Silver panted to them. The shaking was getting steadily worse, but he covered it up the best he could and no-one noticed.

"How should you know? You're just a talking pokemon!" Courtney roared at him, still angry at Sapphire.

"I may be, but...I know what is right...and what is wrong..." he panted before fainting.

"Silver!" Sapphire yelled, scared for her friend. Then, she turned back to the others and growled.

"Looks like someone is angry." Courtney said, smirking a little, "Manectric use-"

"FLAMETHROWER!" Sapphire roared. Chic did the move, making a big hole in the net.

"Flamethrower again!" Right before the attack hit, Manectric let loose a powerful Thunder and shocked Silver badly. As he screamed in pain, Sapphire felt like her world had slowed down. That scream reminded her of Ruby... like they were hurting him instead. Besides, they were horribly hurting her new friend, her... Guardian. She growled even more and brought out Rono.

"Iron Head!" she ordered in rage. She just wanted them gone, not even caring that her pokemon didn't know the move. Rono nodded, building up energy, until he charged. The light that surrounded him was like a Take Down's, except it was black and white and covered his entire body. He had just learned Iron Head.

"Aaaaaaagg RRRROOONNN!" he roared before slamming Ludicolo and sending it flying into Swellow, bringing both pokemon down. Manectric was already defeated from the last attack on it, so he wasn't able to attack back and defend his teammates. Both Admins growled before returning their pokemon. Courtney's bubblegum popped before she said: "You may have won this round, but Team Steam won't go so easy on you next time!"

"Now, goodbye. Until we meet again." Shelly said before they ran away, diving into the bushes. Sapphire stared at where they had disappeared before her pokemon alerted her to Silver. He was groaning slightly, also unconscious, and only being paralyzed with a few burns. She ran over and pet him behind his ears a little. He groaned slightly, but it didn't seem to hurt him. Sapphire then turned to Chic.

"Chic, please see if ya can get anyone ta come and help. I know you, Rono, and some of my other pokemon are strong enough, but I'm afraid you'll jostle him too much." she told her. Chic nodded before jumping off in the direction of Littleroot. Rono looked at Sapphire sadly with some worry on his face.

_Team Steam, who could they be?_ she thought, glancing down at Silver.

* * *

A little while later, Chic came back with Birch and some of his assistants. She had managed to convince them to come since they knew the only Blaziken in the area could be Saph's. Birch grew very worried for his daughter until he saw that she wasn't hurt, but Silver was.

* * *

"Do ya feel better now?" she asked him after he had woken up for the first time. They were in Prof. Birch's lab, where there was all kinds of equipment and several beds for pokemon. He was laying on one while she sat in a chair next to him. He stared at her and asked: "What happened after I was shocked?"

"I fought 'em off with Rono, who just learned Iron Head, and they ran off. But, they mentioned somethin' about a new team before they did."

"New team? Did you catch the name?"

"Yeah." she nodded, "I think they said it was Team Steam or somethin'." Silver froze at the name.

"Team... Steam? Are you sure that's what they said?"

"I'm sure, Silver. What's got ya so uptight all of a sudden?"

"Nothing. It's nothing." he told her, shaking his head, "Could you please leave, though? I still need to rest."

"Okay, but I think yer hidin' somethin'." she told him before walking out and closing the door behind her. Silver sighed before staring blankly ahead and thinking: _If they really are back, then everyone is in danger. Especially Sapphire. I... I can't stay, even though I said I would. But, if I'm going to guard her better this time, I'll need to leave._

* * *

_**Silver's going to leave without telling Sapphire first? What will happen? Will Saph chase after him? Who are the nasty Team Steam, from what we've heard so far? Stay tuned for the next chapter! (I always wanted to say that!) P.S., REVIEW, PEOPLE! I WANT SOME MORE, PLEASE!  
**_


	5. Author's Note

Ruby's Secret

By: Aubrie1234

_**I'm sorry, but I won't be continuing this, as it does not feel right to me anymore. I'm not taking it down or anything, but I'm rewriting it in a new story, **_**Ruby's Secret (Rewritten)_. It'll be a little different, or course, but I hope you like it when I post it._**


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